Single cell type - CCDC25 - The Human Protein Atlas

GENERAL INFORMATIONⁱ General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.
Gene nameⁱ Official gene symbol, which is typically a short form of the gene name, according to HGNC.	CCDC25
Gene descriptionⁱ Full gene name according to HGNC.	Coiled-coil domain containing 25
Predicted locationⁱ All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions. Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached. Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s). The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location. Read more	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	2

HUMAN PROTEIN ATLAS INFORMATIONⁱ Summary of RNA expression and protein localization based on data generated within the Human Protein Atlas project.
Single cell type expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Hepatocytes - Metabolism (mainly)
Single cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Low cell type specificity
Immune cell specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Low immune cell specificity
Immune cell distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in all
Cell line specificityⁱ RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines. Read more	Low cell line specificity
Cell line distributionⁱ RNA distribution category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into five different categories (detected in all, detected in many, detected in some, detected in single and not detected) according to their pattern of detected RNA expression across the panel of cell lines. Read more	Detected in all
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); a Human Protein Atlas antibody- or RNA based score (HPA evidence); and evidence based on PeptideAtlas (MS evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable. Read more	Evidence at protein level

SINGLE CELL TYPESⁱ A summary of single cell RNA (nTPM) from all single cell types. Color-coding is based on cell type groups, each consisting of cell types with functional features in common.
Single cell types Group Expression Alphabetical RNA single cell type specificity: Low cell type specificity

SINGLE CELL TISSUES OVERVIEWⁱ An overview of all tissues where single cell type expression has been analyzed. Each tissue name and corresponding UMAP plot is clickable and redirects to the selected tissue.
Adipose tissue Bone marrow Brain Breast Bronchus Colon Endometrium Esophagus Eye Heart muscle Kidney Liver Lung Lymph node Ovary Pancreas Placenta Prostate Rectum Skeletal muscle Skin Small intestine Spleen Stomach Testis

EXPRESSION CLUSTERING & CORRELATIONⁱ

CCDC25 is part of cluster 2 Hepatocytes - Metabolism with confidenceⁱ 1
205 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell type RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data. Read more	Clusterⁱ ID of the expression cluster of the neighboring gene. Read more
IGSF23	Immunoglobulin superfamily member 23	0.6194	45
ALKBH3	AlkB homolog 3, alpha-ketoglutarate dependent dioxygenase	0.5292	34
OTC	Ornithine carbamoyltransferase	0.5169	2
FAHD2A	Fumarylacetoacetate hydrolase domain containing 2A	0.5137	2
GFER	Growth factor, augmenter of liver regeneration	0.4837	45
TMEM220	Transmembrane protein 220	0.4804	45
MRPL57	Mitochondrial ribosomal protein L57	0.4761	39
BTBD16	BTB domain containing 16	0.4750	34
CIDEB	Cell death inducing DFFA like effector b	0.4741	2
CYP2C19	Cytochrome P450 family 2 subfamily C member 19	0.4717	2
GOLT1A	Golgi transport 1A	0.4636	45
ASAH2	N-acylsphingosine amidohydrolase 2	0.4619	45
ADCY10	Adenylate cyclase 10	0.4594	34
STK16	Serine/threonine kinase 16	0.4590	34
PLA2G12B	Phospholipase A2 group XIIB	0.4583	2

SINGLE CELL TISSUESⁱ Single cell RNA levels of annotated cell type clusters are shown separately for each analyzed tissue. For easier navigation across tissues, use the above Single cell tissue overview, where each tissue name and UMAP plot is clickable and redirects to the selected tissue, alternatively the grey browser on the left side of the window. Barchart shows nTPM levels in each annotated cluster of single cells. To the left, a UMAP plot illustrates the RNA expression profile. The tissue name and plots are clickable and redirect to a more detailed interactive page. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. Please note that the same cell type may be found in several clusters.
Cluster Expression Alphabetical Adipose tissue
Cluster Expression Alphabetical Bone marrow
Cluster Expression Alphabetical Brain
Cluster Expression Alphabetical Breast
Cluster Expression Alphabetical Bronchus
Cluster Expression Alphabetical Colon
Cluster Expression Alphabetical Endometrium
Cluster Expression Alphabetical Esophagus
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Lymph node
Cluster Expression Alphabetical Ovary
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skeletal muscle
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Spleen
Cluster Expression Alphabetical Stomach
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ

Organ

Expression

Alphabetical

Adipocytes	47.5 nTPM
Breast	52.8 nTPM
Adipose tissue	42.2 nTPM

Alveolar cells type 1	25.6 nTPM
Lung	25.6 nTPM

Alveolar cells type 2	38.9 nTPM
Lung	38.9 nTPM

Astrocytes	12.4 nTPM
Brain	12.4 nTPM

B-cells	34.8 nTPM
Liver	74.9 nTPM
PBMC	48.5 nTPM
Stomach	34.5 nTPM
Kidney	33.4 nTPM
Spleen	32.2 nTPM
Bone marrow	29.4 nTPM
Lymph node	27.0 nTPM
Adipose tissue	24.6 nTPM
Colon	22.3 nTPM
Breast	21.3 nTPM

Dendritic cells	31.2 nTPM
Adipose tissue	34.2 nTPM
PBMC	31.8 nTPM
Breast	27.7 nTPM

Endothelial cells	54.2 nTPM
Placenta	80.7 nTPM
Pancreas	77.2 nTPM
Testis	75.5 nTPM
Liver	63.2 nTPM
Breast	63.2 nTPM
Ovary	54.9 nTPM
Skin	50.4 nTPM
Esophagus	50.4 nTPM
Endometrium	44.2 nTPM
Lung	43.7 nTPM
Prostate	42.5 nTPM
Skeletal muscle	41.9 nTPM
Heart muscle	41.4 nTPM
Eye	29.9 nTPM

Fibroblasts	49.3 nTPM
Heart muscle	94.7 nTPM
Lung	59.2 nTPM
Placenta	57.1 nTPM
Breast	52.3 nTPM
Adipose tissue	46.6 nTPM
Esophagus	45.6 nTPM
Skeletal muscle	43.3 nTPM
Ovary	42.5 nTPM
Skin	40.0 nTPM
Stomach	35.6 nTPM
Prostate	25.6 nTPM

Intestinal goblet cells	58.6 nTPM
Small intestine	70.2 nTPM
Rectum	54.2 nTPM
Colon	51.4 nTPM

Macrophages	27.4 nTPM
Lung	57.4 nTPM
Pancreas	53.7 nTPM
Kidney	36.3 nTPM
Testis	30.8 nTPM
Ovary	30.8 nTPM
Endometrium	28.0 nTPM
Breast	25.5 nTPM
Prostate	25.3 nTPM
Spleen	21.8 nTPM
Adipose tissue	21.4 nTPM
Skeletal muscle	20.1 nTPM
Bone marrow	17.5 nTPM
Esophagus	17.3 nTPM
PBMC	13.6 nTPM
Stomach	11.7 nTPM

Paneth cells	51.1 nTPM
Rectum	61.7 nTPM
Small intestine	48.8 nTPM
Colon	42.8 nTPM

Plasma cells	40.7 nTPM
Spleen	54.4 nTPM
Esophagus	49.4 nTPM
Stomach	42.7 nTPM
Bone marrow	36.2 nTPM
Adipose tissue	20.6 nTPM

Respiratory ciliated cells	53.7 nTPM
Lung	71.4 nTPM
Bronchus	36.0 nTPM

Smooth muscle cells	49.1 nTPM
Heart muscle	109.0 nTPM
Bronchus	88.4 nTPM
Pancreas	57.7 nTPM
Esophagus	46.5 nTPM
Breast	43.3 nTPM
Adipose tissue	40.3 nTPM
Skeletal muscle	36.6 nTPM
Ovary	31.3 nTPM
Skin	30.7 nTPM
Prostate	29.3 nTPM
Endometrium	27.2 nTPM

T-cells	38.7 nTPM
Kidney	56.2 nTPM
PBMC	47.4 nTPM
Ovary	46.7 nTPM
Esophagus	45.9 nTPM
Liver	44.4 nTPM
Colon	41.3 nTPM
Bone marrow	40.8 nTPM
Skeletal muscle	40.3 nTPM
Adipose tissue	40.0 nTPM
Stomach	39.3 nTPM
Lung	38.0 nTPM
Skin	35.0 nTPM
Spleen	34.0 nTPM
Lymph node	33.3 nTPM
Breast	31.4 nTPM
Endometrium	29.9 nTPM
Prostate	14.2 nTPM

Basal prostatic cells	39.6 nTPM
Prostate	39.6 nTPM

Basal squamous epithelial cells	55.2 nTPM
Esophagus	55.2 nTPM

Cholangiocytes	60.1 nTPM
Liver	60.1 nTPM

Collecting duct cells	53.3 nTPM
Kidney	53.3 nTPM

Undifferentiated cells	71.2 nTPM
Small intestine	98.3 nTPM
Colon	59.7 nTPM
Rectum	55.5 nTPM

Adipose tissue

Bone marrow

Brain

Breast

Bronchus

Colon

Endometrium

Esophagus

Eye

Heart muscle

Kidney

Liver

Lung

Lymph node

Ovary

Pancreas

Placenta

Prostate

Rectum

Skeletal muscle

Skin

Small intestine

Spleen

Stomach

Testis

PBMC